Negi and Chisame - Racan's place
Chachamaru, Kazumi and Sayo - Boarding at the train
Asuna, Setsuna, Konoka, Kaede - some town where they were bounty hunting
Nodoka - with a treasure group
Yue - in a magic school
Kotaro, Akira, Ako, Natsumi - in the tournament
Makie and Yuna - somewhere in a restaurant

Nope... Ayaka didn't join Negi... she even told Asuna that she would be left behind because I think she knew that it was kinda dangerous... seeing as how Asuna overpowered her when they were equals before...

the twins... I think I remembered them joining at least until Yuna, Makie, Ako and Akira started running towards the teleportation spell...